I discovered Premier Biosoft's Array Designer while I ran the core facility in Rockefeller University. I used it there for several years for all microarray primer and probe design needs. When I moved to Mount Sinai, I acquired it again and continue to use it. Array Designer supports both expression microarray and SNP genotyping arrays. The designed primers and probe have produced excellent results for me.
I found the Array Designer intuitive to use. The streaming multimedia tour made it easy to get started. To begin the design process, a large number of sequences can be imported either directly from Entrez by specifying the accession numbers or from the local drive as long as they are in Genbank and FASTA formats. The built-in interpreter saves you time by converting the GenBank annotations into a table of known SNP's. According to PREMIER Biosoft documentation, the default parameters have been selected based on considerable research and private communications with experts. I generally rely on them and have had to change them only in particularly challenging situations. The project management functionality has helped me stay organized.
The high success rate of design may, in part, be due to the use of BLAST for avoiding cross homologies. To design specific probes or primers automatically, you simply ask Array Designer to connect to the appropriate database. It will BLAST all templates against it and interpret results to identify significant homologies in each and avoid them during oligo search. You can use the public databases for this purpose, though the search speed they offer may be inadequate for large projects. For better speed, Array Designer supports local databases. It is fairly easy to set them up, either copying the public databases or using your own sequence data. Finding the best possible primers or probes also contributes to the high success rate. According to PREMIER Biosoft documentation, the entire sequence is taken into consideration and every possible oligo within the specified length range is rated based on property calculations.
PREMIER Biosoft announced the release of version 4 to meet the challenges of the post- HGP era. It now offers new capabilities called Tiling Arrays and Whole Genome Arrays. Tiling arrays enable you design microarrays by spotting both intragenic and intergenic sequences to study control elements including protein binding sites. To avoid spotting repetitive regions, you can mask the input sequence using any of the available resources like Repetitive Masker. For transcriptome analysis, you can load complete medium size genomes, chromosomes or long contigs using the Whole Genome Array feature. Array Designer automatically BLAST's each gene or exon against the input genome to design highly specific probes. I am looking forward to using these new capabilities.
Greg Khitrov. Ph.D.
Director, Life Science Technology Laboratory
Mount Sinai School of Medicine